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RevertSam in BamRealigner: Failed to write bam

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    Genevieve Brandt (she/her)

    Hi Claudia Chu,

    Looking at this issue, it seems that it might be a problem with the WDL because there is an issue writing the output file. If you do find that you still get the java.lang.NullPointerException with the individual Picard command, we can do further digging to determine what the issue is with RevertSam.

    Our GATK support team is focused on GATK specific questions and questions regarding GATK abnormal results. Here is our support policy for more information. You can leave this post here in case other users can provide insight and you can also check out these resources for more information:

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    Claudia Chu

    Hi Genevieve Brandt,

    It's a bug in the WDL. In the GenerateOutputMap, it is using the incorrect grep regex to retrieve the read groups.

    # in the current WDL
    grep '@RG'


    # Recommended from https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
    grep '^@RG'

    This made it generate an output map that included the "bwa" read group names because "@RG" was in the line, but not at the beginning. If I manually removed the "bwa" read groups from the output_map.tsv file, it runs. Can we update the current WDL in GPTAG/BamRealigner?

    Additionally, RevertSam checks if the read groups are valid (picard.sam.RevertSam$ValidationUtil.assertAllReadGroupsMapped), but it did not stop here even though the output_map included invalid read group names. It would be helpful to update this as well so similar bugs can be easier to catch. 

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    Samantha (she/her)

    Hi Claudia Chu,

    I would suggest reaching out to the owners of that WDL for any requests to update it. I also noticed the WDL you linked was version 14 - have you tried running the most recent version (18)?

    Best,

    Samantha

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    Claudia Chu

    Hi Samantha

    I talked to the owners of the WDL and they made the update in version 19. Thanks!

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